# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: pfam_list/zf-GRF.hmm.txt
# target sequence database: proteomes/Pan_troglodytes.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: zf-GRF [M=45]
Accession: PF06839.12
Description: GRF zinc finger
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.4e-37 126.6 10.7 1.4e-19 70.3 0.8 4.2 4 tr|H2QQG8|H2QQG8_PANTR Nei like DNA glycosylase 3 OS=Pa
2.4e-36 123.9 20.9 2.7e-19 69.3 4.0 3.3 3 tr|H2R419|H2R419_PANTR DNA topoisomerase OS=Pan troglod
2.2e-17 63.2 8.2 2.2e-17 63.2 8.2 2.5 2 tr|A0A2J8Q5V4|A0A2J8Q5V4_PANTR ERI1 exoribonuclease family memb
3.5e-15 56.2 2.2 3.5e-15 56.2 2.2 2.8 2 tr|H2QPA8|H2QPA8_PANTR ZCCHC4 isoform 1 OS=Pan troglody
1.9e-13 50.6 0.3 5.2e-13 49.2 0.3 1.8 1 tr|A0A2J8M271|A0A2J8M271_PANTR ZGRF1 isoform 3 OS=Pan troglodyt
5e-13 49.3 0.5 1.6e-12 47.7 0.5 1.9 1 tr|K6ZDW9|K6ZDW9_PANTR DNA-(apurinic or apyrimidinic si
4.7e-06 26.9 2.5 4.7e-06 26.9 2.5 2.4 2 tr|H2PZS1|H2PZS1_PANTR TTF2 isoform 1 OS=Pan troglodyte
Domain annotation for each sequence (and alignments):
>> tr|H2QQG8|H2QQG8_PANTR Nei like DNA glycosylase 3 OS=Pan troglodytes OX=9598 GN=NEIL3 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.4 0.1 4.3 1.4e+04 25 30 .. 234 239 .. 233 240 .. 0.80
2 ? -1.3 7.0 0.92 3e+03 4 33 .. 255 283 .. 253 287 .. 0.75
3 ! 70.3 0.8 4.1e-23 1.4e-19 2 44 .. 508 551 .. 507 552 .. 0.93
4 ! 69.4 3.2 8e-23 2.6e-19 1 44 [. 554 597 .. 554 598 .. 0.97
Alignments for each domain:
== domain 1 score: -3.4 bits; conditional E-value: 4.3
zf-GRF 25 FYkCpk 30
FY+C k
tr|H2QQG8|H2QQG8_PANTR 234 FYRCRK 239
9***65 PP
== domain 2 score: -1.3 bits; conditional E-value: 0.92
zf-GRF 4 kcg.rlavlltvrktgpNkGRkFYkCpkgke 33
+cg +++ + r g N+ R Y Cp +++
tr|H2QQG8|H2QQG8_PANTR 255 NCGqCHCRITVCR-FGDNN-RMTYFCPHCQK 283
6994456666665.99997.88888**9986 PP
== domain 3 score: 70.3 bits; conditional E-value: 4.1e-23
zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
C + rl+ l++vrk+g+NkGR+FY+Cp+++e+qCgFF+Wad
tr|H2QQG8|H2QQG8_PANTR 508 RCSkHNRLCILRVVRKDGENKGRQFYACPLPREAQCGFFEWADL 551
688688************************************95 PP
== domain 4 score: 69.4 bits; conditional E-value: 8e-23
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
p+C++g+++ ++tv k gpN+G++F++Cp+gkekqC+FF+Wa++
tr|H2QQG8|H2QQG8_PANTR 554 PFCNHGKRSIMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAEN 597
68***************************************986 PP
>> tr|H2R419|H2R419_PANTR DNA topoisomerase OS=Pan troglodytes OX=9598 GN=TOP3A PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.4 0.3 1 3.4e+03 3 16 .. 658 672 .. 656 675 .. 0.75
2 ! 64.0 3.4 3.8e-21 1.2e-17 1 44 [. 811 851 .. 811 852 .. 0.96
3 ! 69.3 4.0 8.2e-23 2.7e-19 2 45 .] 896 939 .. 895 939 .. 0.97
Alignments for each domain:
== domain 1 score: -1.4 bits; conditional E-value: 1
zf-GRF 3 Ck.cgrlavlltvrk 16
C+ c + vl+t ++
tr|H2R419|H2R419_PANTR 658 CPqCNKDMVLKTKKN 672
888889999988864 PP
== domain 2 score: 64.0 bits; conditional E-value: 3.8e-21
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWade 44
++C+cg++avlltvrk+gpN+GR+F+kC+ g+ C+FF Wad+
tr|H2R419|H2R419_PANTR 811 VTCNCGQEAVLLTVRKEGPNQGRQFFKCNGGS---CNFFLWADS 851
58****************************99...********7 PP
== domain 3 score: 69.3 bits; conditional E-value: 8.2e-23
zf-GRF 2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWadek 45
+C c +++v++tv+k+gpNkGR+F++C+k++e+qCgFF+W+de+
tr|H2R419|H2R419_PANTR 896 SCLCSQPSVTRTVQKDGPNKGRQFHTCAKPREQQCGFFQWVDEN 939
7*****************************************96 PP
>> tr|A0A2J8Q5V4|A0A2J8Q5V4_PANTR ERI1 exoribonuclease family member 2 OS=Pan troglodytes OX=9598 GN=ERI2 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -0.1 0.1 0.4 1.3e+03 32 43 .. 49 61 .. 46 63 .. 0.77
2 ! 63.2 8.2 6.6e-21 2.2e-17 1 44 [. 502 549 .. 502 550 .. 0.97
Alignments for each domain:
== domain 1 score: -0.1 bits; conditional E-value: 0.4
zf-GRF 32 ke.kqCgFFkWad 43
+e k C F W d
tr|A0A2J8Q5V4|A0A2J8Q5V4_PANTR 49 SEvKLCAFVTWSD 61
44588******98 PP
== domain 2 score: 63.2 bits; conditional E-value: 6.6e-21
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgke....kqCgFFkWade 44
plCkcgr++++l+v+++gpN+G+ FY+Cp gk+ k+Cg+FkW+++
tr|A0A2J8Q5V4|A0A2J8Q5V4_PANTR 502 PLCKCGRRSKRLVVSNNGPNHGKVFYCCPIGKYqenrKCCGYFKWEQT 549
79******************************999***********96 PP
>> tr|H2QPA8|H2QPA8_PANTR ZCCHC4 isoform 1 OS=Pan troglodytes OX=9598 GN=ZCCHC4 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 56.2 2.2 1.1e-18 3.5e-15 1 45 [] 38 82 .. 38 82 .. 0.96
2 ? -5.1 4.2 7 2.3e+04 21 36 .. 402 415 .. 391 420 .. 0.78
Alignments for each domain:
== domain 1 score: 56.2 bits; conditional E-value: 1.1e-18
zf-GRF 1 plCkcg.rlavlltvrktgpNkGRkFYkCpkgke.kqCgFFkWadek 45
plC++g +l+++++ +g++++R FY+C+++++ k+C+FF+W+dek
tr|H2QPA8|H2QPA8_PANTR 38 PLCPHGpTLLFVKVT--QGKEETRRFYACSACRDrKDCNFFQWEDEK 82
79*************..6***************************95 PP
== domain 2 score: -5.1 bits; conditional E-value: 7
zf-GRF 21 kGRkFYkCpkgkekqC 36
GRk+ C ++k+ C
tr|H2QPA8|H2QPA8_PANTR 402 DGRKWNHCFLCKK--C 415
6888888888886..5 PP
>> tr|A0A2J8M271|A0A2J8M271_PANTR ZGRF1 isoform 3 OS=Pan troglodytes OX=9598 GN=ZGRF1 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 49.2 0.3 1.6e-16 5.2e-13 1 43 [. 1347 1389 .. 1347 1391 .. 0.95
Alignments for each domain:
== domain 1 score: 49.2 bits; conditional E-value: 1.6e-16
zf-GRF 1 plCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43
p+C + ++a+l v+k+gpNkGR FY+C +k C FFkW +
tr|A0A2J8M271|A0A2J8M271_PANTR 1347 PSCHHSQPAKLVMVKKEGPNKGRLFYTCDGPKADRCKFFKWLE 1389
68***************************************87 PP
>> tr|K6ZDW9|K6ZDW9_PANTR DNA-(apurinic or apyrimidinic site) lyase OS=Pan troglodytes OX=9598 GN=APEX2 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 47.7 0.5 4.7e-16 1.6e-12 1 42 [. 467 515 .. 467 517 .. 0.94
Alignments for each domain:
== domain 1 score: 47.7 bits; conditional E-value: 4.7e-16
zf-GRF 1 plCk.cgrlavlltvrktgpNkGRkFYkCpkgke......kqCgFFkWa 42
plC + +++v++tv+k gpN GR FY C+ +++ + C+FF W
tr|K6ZDW9|K6ZDW9_PANTR 467 PLCGgHREPCVMRTVKKPGPNLGRRFYMCARPRGpptdpsSRCNFFLWS 515
6899777***************************99999999******5 PP
>> tr|H2PZS1|H2PZS1_PANTR TTF2 isoform 1 OS=Pan troglodytes OX=9598 GN=TTF2 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 26.9 2.5 1.4e-09 4.7e-06 2 38 .. 5 39 .. 4 41 .. 0.89
2 ? -0.5 0.5 0.54 1.8e+03 22 43 .. 72 96 .. 66 98 .. 0.73
Alignments for each domain:
== domain 1 score: 26.9 bits; conditional E-value: 1.4e-09
zf-GRF 2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38
C+ +g++++l+t ++gpNkG+ FY+C + C F
tr|H2PZS1|H2PZS1_PANTR 5 RCPeHGTFCFLKTGVRDGPNKGKSFYVCRADT---CTF 39
6999*********999************8765...766 PP
== domain 2 score: -0.5 bits; conditional E-value: 0.54
zf-GRF 22 GRkFYkCpkgke...kqCgFFkWad 43
R F++C k + Cg W d
tr|H2PZS1|H2PZS1_PANTR 72 YRLFFRCIRSKAegkRWCGSIPWQD 96
599****766655566799888877 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (45 nodes)
Target sequences: 23008 (11942255 residues searched)
Passed MSV filter: 1193 (0.0518515); expected 460.2 (0.02)
Passed bias filter: 430 (0.0186892); expected 460.2 (0.02)
Passed Vit filter: 21 (0.000912726); expected 23.0 (0.001)
Passed Fwd filter: 7 (0.000304242); expected 0.2 (1e-05)
Initial search space (Z): 23008 [actual number of targets]
Domain search space (domZ): 7 [number of targets reported over threshold]
# CPU time: 0.10u 0.01s 00:00:00.11 Elapsed: 00:00:00.07
# Mc/sec: 7677.16
//
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